Molecular techniques and their limitations shape our view of the holobiont

Ira Cooke; Oliver Mead; Casey Whalen; Chloë Boote; Aurelie Moya; Hua Ying; Steven Robbins; Jan M Strugnell; Aaron Darling; David Miller; Christian R Voolstra; Maja Adamska; Consortium of Australian Academy of Science Boden Research Conference Participants

doi:10.1016/j.zool.2019.125695

Molecular techniques and their limitations shape our view of the holobiont

Zoology (Jena). 2019 Dec:137:125695. doi: 10.1016/j.zool.2019.125695. Epub 2019 Jul 16.

Affiliations

¹ Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia. Electronic address: ira.cooke@jcu.edu.au.
² ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, 2601, Australia; Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia.
³ Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia.
⁴ Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia.
⁵ Australian Center for Ecogenomics, University of Queensland, St. Lucia, QLD, 4072, Australia.
⁶ Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre of Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, 4810, QLD, Australia; Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, 3083, Australia.
⁷ The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
⁸ Department of Biology, University of Konstanz, Konstanz, 78457, Germany.

PMID: 31759226
DOI: 10.1016/j.zool.2019.125695

Abstract

It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.

Keywords: Evolutionary inference; Holobiont; Imaging; Metagenomic sequencing; Model system; Multi-omics.

Publication types

Review

MeSH terms

Environmental Microbiology*
Microbiota*
Symbiosis*